anndata

Single-cell analysis in Python. Scales to >100M cells.

Annotated data.

rapids-singlecell: GPU-accelerated framework for scRNA analysis

Single-cell perturbation analysis

muon is a multimodal omics Python framework

Multi-agent LLM driven cell type annotation for single-cell RNA-Seq data

Multimodal Data (.h5mu) implementation for Python

Unsupervised Deep Disentangled Representation of Single-Cell Omics

Feature-rich Python implementation of the tximport package for gene count estimation.

The AnnSQL package enables SQL based queries on AnnData objects.

pseudobulking on an AnnData object

An AnnData-based framework for integrated proteomics analysis

Search- and quantification-engine agnostic biological interpretation of proteomics data

Scalable framework for integrating single-cell omics with genetic data using AnnData.

scXpand: detection of T-cell clonal expansion from single-cell RNA sequencing

A user-friendly library that brings familiar DataFrame-style operations to AnnData objects with a simple and expressive API.

Download and Convert METASPACE datasets to common formats such as AnnData or SpatialData

Scientific Agent for evidence-grounded evaluation of cell-therapy products.

Dataloader for common proteomics search engine outputs into AnnData format